Manuel Rodríguez-Pascual

Improvements on the Fusion Code FAFNER2

FAFNER2, which is a 3-D code adapted to the TJ-II helical axis stellarator from the original one developed by Lister at Max Planck IPP, simulates by Monte Carlo methods the neutral beam injection technology (a key heating method for most of the fusion experiments worldwide). To date, FAFNER2 has been usually run at CIEMAT by means of a batch mode on a shared memory computer with MIPS processors. This paper describes how the application has ben updated to employ MPI and run on standard Linux clusters. As in Grid infrastructures, not every site has MPI installed on their nodes; a serial version has also been developed, together with a Java Distributed Resource Management Application API program able to run FAFNER2 on distributed resource platforms, such as Grid infrastructures. In addition, and with new improvements in the code for maximizing its performance, the metascheduler GridWay has also been incorporated for maximizing the executions on the Grid. Scalability, fault tolerance, and correctness of the result have been proved employing a significant number of particles and nodes within a local cluster and the EGEE infrastructure.

More Efficient Executions of Monte Carlo Fusion Codes by Means of Montera: The ISDEP Use Case

ISDEP (Integrator of Stochastic Differential Equations for Plasmas) is a Monte Carlo code that solves the plasma dynamics in a fusion device and perfectly scales on distributed computing platforms. Montera is a recent framework developed for achieving Grid efficient executions of Monte Carlo applications, as ISDEP is. In this work, the improvement of performing the calculations of ISDEP with Montera, which rise up to 34.9%, is shown as well as an analysis on the implications it could have, which aim to show to the fusion research community the benefits of using Montera.

Drift Kinetic Equation Solver for Grid (DKEsG)

Neoclassical (NC) transport calculations are necessary for the complete simulation cycle of the behavior of plasmas inside both tokamaks and stellarators, which are more complex to be performed on the latest. In addition, due to the fact that the NC transport is mainly determined by the magnetic properties of the device (mathematically designed by the number of Fourier harmonics needed to describe the confining magnetic field), its study is mandatory to ensure the efficiency of a certain coil configuration before it is implemented in a fusion reactor. Thus, improvements to the already constructed devices and certain design decisions for the new ones, such as W7-X, NCSX, or QPS, have been made based on the estimations of the NC transport, among other criteria. In this sense, a compromise between the number of modes and polynomials to describe the distribution function and the required computing time to obtain reliable estimates is a must. This paper presents the porting process to the Grid and the computational optimization of the Drift Kinetic Equation Solver code, devoted to obtain the monoenergetic diffusion coefficients of the NC transport as well as the first coupled prototype for estimating the transport coefficients with such a new code release. The advantage of this code over the Monte Carlo applications already in production on the Grid is that it allows the estimation of all the transport coefficients, not only the diagonal ones. The tests and results obtained have been applied to the TJ-II Flexible Heliac, a stellarator in operation at National Fusion Laboratory (Spain), by using the EELA-2 Project infrastructure.

gGEM: A Gyrofluid Model to be Used on Distributed Platforms

The study of core turbulence represents a key line of research in fusion plasmas. By adding collisions and electromagnetic induction to the parallel dynamics of the standard six-moment toroidal model, it is possible to study the gyrofluid electromagnetic phenomena in the context of edge turbulence with the GEM code. Currently, the code describes the fluctuation free-energy conservation in a gyrofluid model by means of the polarization equation which relates the ExB flow and eddy energy to the combinations of the potential, the density, and the perpendicular temperature. To do so, supercomputers have been used only to date. In this paper, we demonstrate its feasibility as a cluster application on a production environment based on any kind of distributed memory, enhancing in this way its scope. The scalability (which grows linearly with a correlation factor of 0.99978) and the correctness of our solution with respect to the previous GEM version have been evaluated in a local cluster of 88 nodes. The fault tolerance and the Grid suitability have been demonstrated by executing our application in the EUrope Fusion for ITER Applications infrastructure by adapting the code to this paradigm and by improving its parallel Grid performance. It can be employed on its own or belonging to workflows in order to perform a wider more complex analysis of fusion reactors.

Simulations of fast ions distribution in stellarators based on coupled Monte Carlo fuelling and orbit codes

The numerical simulation of the dynamics of fast ions coming from neutral beam injection (NBI) heating is an important task in fusion devices, since these particles are used as sources to heat and fuel the plasma and their uncontrolled losses can damage the walls of the reactor. This paper shows a new application that simulates these dynamics on the grid: FastDEP. FastDEP plugs together two Monte Carlo codes used in fusion science, namely FAFNER2 and ISDEP, and add new functionalities. Physically, FAFNER2 provides the fast ion initial state in the device while ISDEP calculates their evolution in time; as a result, the fast ion distribution function in TJ-II stellerator has been estimated, but the code can be used on any other device. In this paper a comparison between the physics of the two NBI injectors in TJ-II is presented, together with the differences between fast ion confinement and the driven momentum in the two cases. The simulations have been obtained using Montera, a framework developed for achieving grid efficient executions of Monte Carlo applications.

Performance improvements for the neoclassical transport calculation on Grid by means of pilot jobs

The neoclassical transport is a lower limit of the whole transport in plasmas confined in fusion devices, either stellarators or tokamaks. Even more, the determination of a vast database compiling monoenergetic and transport coefficients is very useful for coupling different codes, which can use those values as input data. The DKEsG application is able to obtain such parameters on Grid infrastructures. Since a large number of regular jobs are needed for filling the aforementioned database, a fast and robust execution scheme is necessary. For this purpose, a new DRMAA-enabled DKEsG version that makes use of a new generic pilot-job platform is used, avoiding the most significant overheads related to standard Grid middleware. This new developed mechanism is suitable for many other scientific applications involving high-throughput calculations.

FAFNER2: A comparison between the Grid and the MPI versions of the code

FAFNER2 is a 3D code that simulates by Monte Carlo methods the Neutral Beam Injection (NBI) technology. The original version was implemented for shared memory computers with MIPS proccesors, so an update to be executed by means of MPI on standard Linux clusters has been carried out as well as a new version to be run on Grid. To do the latest, a serial version has also been developed, together with a Java DRMAA program that is submitted by the GridWay metascheduler. As a result, two new improved versions of the code (HPC and Grid) are available.

The Latin American Giant Observatory: A Successful Collaboration in Latin America Based on Cosmic Rays and Computer Science Domains

In this work the strategy of the Latin American Giant Observatory (LAGO) to build a Latin American collaboration is presented. Installing Cosmic Rays detectors settled all around the Continent, from Mexico to the Antarctica, this collaboration is forming a community that embraces both high energy physicist and computer scientists. This is so because the data that are measured must be analytical processed and due to the fact that a priori and a posteriori simulations representing the effects of the radiation must be performed. To perform the calculi, customized codes have been implemented by the collaboration. With regard to the huge amount of data emerging from this network of sensors and from the computational simulations performed in a diversity of computing architectures and e-infrastructures, an effort is being carried out to catalog and preserve a vast amount of data produced by the water-Cherenkov Detector network and the complete LAGO simulation workflow that characterize each site. Metadata, Permanent Identifiers and the facilities from the LAGO Data Repository are described in this work jointly with the simulation codes used. These initiatives allow researchers to produce and find data and to directly use them in a code running by means of a Science Gateway that provides access to different clusters, Grid and Cloud infrastructures worldwide.

A Comparative Analysis of Adaptive Solutions for Grid Environments

Grid computing environments are distributed systems composed by heterogeneous and geographically distributed resources. This type of systems mainly emerged to satisfy the increasing computing power demand within the scientific community. Despite the advantages of such paradigm, there are still several challenges related to the discovery, monitoring and selection of grid resources. Moreover, the dynamic nature and changing characteristics of such environments worsen the applications performance. Thus, improving their efficiency is a fundamental issue. The present contribution analyses two self-adaptive solutions focused on enhancing the grid resource selection process by using resources in an efficient way. On the one hand, the Efficient Resources Selection model which is defined from the user’s point of view (it avoids controlling or modifying the infrastructure) and it is based on the Scatter Search method for achieving a suitable selection of resources. On the other hand, Montera2, a framework designed for addressing an efficient execution of distributed applications on the grid; it defines and employs a dynamic scheduling algorithm to determine the size and number of tasks to be executed. Both approaches have been tested on a real European infrastructure belonging to the well-known European Grid Infrastructure (EGI) project. The study also compares both solutions with the standard scheduling technique that governs this infrastructure, the gLiteWMS scheduler, showing a much better performance by reducing the final makespan by a factor of 20 if compared to the gLiteWMS scheduler. An analysis of task and time overheads for both approaches is also included. Furthermore, comparisons with many other solutions proposed in the literature are presented, showing the advantages of our approaches.

A Fault Tolerant Workflow for Reproducible Research

In this work, the authors present a set of tools to overcome the problem of creating and executing distributed applications on dynamic environments in a resilient way, also ensuring the reproducibility of the performed experiments. The objective is to provide a portable, unattended and fault-tolerant set of tools, encapsulating the infrastructure-dependent operations away from the application developers and users, allowing to perform experiments based on open access data repositories. In this way, users can seamlessly search and lately access datasets that can be automatically retrieved as input data into a code already integrated in the proposed workflow. Such a search is based on metadata standards and relies on Persistent Identifiers (PID) to assign specific repositories. The applications profit from Distributed Toolbox, a newly created framework devoted to the creation and execution of distributed applications and includes tools for unattended Cluster and Grid execution, where a total fault tolerance is provided. By decoupling the definition of the remote tasks from its execution and control, the development, execution and maintenance of distributed applications is significantly simplified with respect to previous solutions, increasing their robustness and allowing running them on different computational platforms with little effort. The integration with open access databases and employment of PIDs for long-lasting references ensures that the data related to the experiments will persist, closing a complete research circle of data access / processing/ storage / dissemination of results.